Molly Hooper: Agent of SHIELD
by Anna-san
Summary: Molly Hooper is thrown in for a loop when she's been plucked out of the Hub to spy on Sherlock Holmes to assess his potential to be a SHIELD recruit.
1. Chapter 1

**Disclaimer:** I really don't own anything :p

**A/N:** Hi. This is my first fic for these fandoms because I had an itch to write about Molly being a spy. So sorry to the followers of my other 2 crossovers, I'm not dropping those but the muses have led me to my current obsessions, Sherlock and the MCU. They don't have an MCU category here yet, by the way, so this is under the Avengers and Sherlock crossover category.

**Chapter 1**

She crosses her legs as she leans on the corner of the diner booth. Her fingers were playing with the edges of the manila folder on the table. The waitress puts down the cup and saucer and pours the steaming brown liquid. The sugar and cream follows after. The woman in the booth uncrosses her legs to fix her coffee the way she liked it. Her peripheral had caught sight of the man in the leather trench coat. He jogs a bit as the rain outside started to pour. The diner bell rings as the dark man with the heavy coat enters and looks around before spotting the woman in the corner of the diner. He shrugs his coat to shake off the water and swiftly walks toward the woman. She wasn't hard to spot. Her red locks would always standout anywhere. He slides on the opposite seat across from her and she slides the folder to him.

"That didn't take too long, didn't it?" Nick Fury starts as he opens the report.

"I don't see how this man could be SHIELD material. He's not even the same level as Stark." Natasha Romanov takes a sip of her coffee with one hand as the other drums its fingers on the table. Fury doesn't look up as he kept reading the file.

"He's an exceptional person. I've seen him in action with Scotland Yard with that Daniels case, " Natasha was about to cut him off but Fury continues, "But yeah, he doesn't play well with others like your last recommendation.

"His brain works 10 times faster than the normal person can but he can't be motivated to work for us." She rests head against her perched arm on the window pane with her eyes staring at the droplets on the glass.

"Says here he likes puzzles. That's a way in." Fury puts down the file and rests is right hand on the table.

"Yeah… But that just means we need to be always a few steps ahead. I don't have that time and patience."

"I take it that he's not the kind of man that you can persuade with your assets either…" Fury smirks as he leans forward to rest his head on his clasped hands where his elbows are rests on the table.

"Oh god no!" She exclaims. She combs back her hair with her right hand.

This assignment had her in England for a week to follow and scout for the one and only consulting detective as a possible recruit. Fury had flagged him after his visit to London a few months back. He saw potential and had his best agent to look into it. Natasha was intrigued at first but after a week of seeing this Sherlock Holmes from a vantage point, she concluded that a direct approach from her was not the best course of action. In her honest opinion, Fury was wasting his time. Holmes is a loose cannon and he would bypass most of the SHIELD training with his annoying wit and powers of deduction. He might possible scare away other personnel in the process. The man was not worth the trouble.

But if Fury would insist, she put an alternative recommendation at the end of the report.

"Then we'll get someone else. But I think she's overqualified for this, Romanov. It's also not her skill strength. She only goes undercover for short missions. " Fury takes a beat waiting for her to expound more on the alternative recommendation.

"I know. But I have a plan," Natasha meets his eye with a smirk. He only raises his brow and mirrors her knowing smile.

"Then I can trust you to handle her training." He slides off the bench and stands up, signaling the end of their meeting.

Natasha looks up and slightly nods. "I'll leave for the Hub in a few hours. But clear it with Hand. She hates surprises."

Fury rolls his eyes and proceeds to leave. Natasha's eyes follow his back as he heads back out in the rain. Right on time, a black SUV arrives in front of the diner. She grabs the folder and tucks it under her jacket. She waits out the rain before heading out to the airstrip.

She takes out her phone as she walks to her ride parked a few blocks away.

It takes a few rings before the other person picks up.

"Hello? Natasha?" a voice with a proper English accent calls from the other line.

"Hey there Dr. Hooper," Natasha coyly uses her proper title.

"I thought you were in England. Are you still there now? I haven't been back there in ages. Do you have time to see the sights? " Dr. Hooper loads all her questions to Natasha and the redhead only chuckles in amusement.

"I was but I'm back in New York so no, I'm not there anymore. I didn't see much but I'm sure you'll get the opportunity to go back soon and see some sights yourself. Listen, I'll be in the Hub in a few hours. I'll fill you in with the details then."

"What?" The person on the other line exclaims. "What does that—" Natasha smirks as she hangs up the phone. She gets in her car and drives to the airstrip where a quintjet was waiting to take her to the Hub.

**_tbc_**

**A/N:** This is also published in my AO3 account under geishakamameha and my tumblr account with the same name. There's already 4 chapters there so check it out there too. I want some feedback too. Be constructive and I'll try my best to be more critical. :D


	2. Chapter 2

**Disclaimer:** I really don't own anything :p

**A/N:** I'm gradually adding the chapters I've already written since I write the author's notes in the doc manager area. If you check out my tumblr or my AO3 account, there's already 4 chapters there. Look for geishakamameha. :D

**Chapter 2**

"Okay, run this by me again?" Molly Hooper shakes her head in disbelief and denial. She tries to appear busy fiddling with the test tubes and flasks on the lab desk in front of her. She didn't want to directly look at Natasha who was tilting her head in amusement at her discomfort.

Natasha presses her palms on the table as she leans in. "London, undercover, Sherlock Holmes… I'll give you time to process." She smirks as Molly furrows her brows in with a glare that was intended to look intimidating except she just looked like a kid who didn't get her way.

"But isn't this more your wheelhouse? You just did it with Tony Stark some time ago…" Molly stops fidgeting and slumps on the rotating stool near Natasha.

"You know, I wouldn't recommend you to do this if you aren't qualified." Natasha takes the other stool and slides it beside Molly's. "Besides, this will be very different from your usual assignments." She takes the folder containing the brief and slides it to Molly. The doctor places her hand tentatively over it and painstakingly opens it. She wants to drag it out so she shuts her eyes tightly and releases the breath she didn't know she was holding.

The first thing she reads is the undercover alias. Her head zooms to look at Natasha's face and gives her a horrified look. "Is this a fuckin' joke, Romanov?" She takes the first page of the brief as the rest of the folder falls to the floor, scattering all over. She holds the page, crumpling the top with her tightly clenched fist.

"Nop-puh," the redhead pops the p. She tilts her head, trying to act cute and smiles.

"Molly Hooper is not an alias! That is my real name!" Molly starts pacing. "I'm not going back to London as myself! This is has to be against SHIELD protocol…" Her frantic mind is recalling scenarios of her childhood in England. She was a loner and a pariah because of her intellect and was always ignored or bullied by her peers. It was hard fitting in anywhere since she was too smart to be with kids her own age and being advanced 3 years in her secondary schooling had her picked on by the older kids. Her relief came when she entered university at 15 but only to lose her father after graduating 3 years later. After finishing medical school at 22, she gets recruited by SHIELD as part of a medical research team. Her first assignments were in the Fridge, studying the different people who have come in contact with radiation. Sometimes she was sent on field to retrieve and contain these people. After her almost fatal encounter with a hostile subject, she was transferred to DC in the Triskelion. She was put more on field to hone her skills in order to avoid future incidents when encountering aggressive enemies. After 5 years of fieldwork, she requests a transfer to a quiet lab space in the Hub, deciding that she wanted to do more research and publish papers as Dr. Molly Hooper. Most of her papers were of the forensic type. She left out the details about her encounters as a SHIELD agent but most of her data came from her time in the field.

Molly was finally in a relatively calm and quiet place in her SHIELD career. Natasha was putting her back out there with this mission. And to top it off, she had to be herself. After several minutes of pacing, she turns to Natasha who was able to save the papers from being trampled on by her frantic feet. The spy holds out the folder in her hand, waiting for Molly to calm down.

"Read the brief before you go ballistic, okay?" The doctor narrows her eyes at her and snatches the folder from her hand.

She skims the file only to read a highly detailed backstory that was nearly identical to her own, a profile of her undercover personality, and even a list of her appearance that needed to change. She huffs a bit after reading the part of 'being a pushover by being very accommodating to her workmates'. She licks her lips and bites it after glaring at Natasha some more. "This…" she says holding up the folder, "is laying it on pretty thick. And a lot of your profile is not even me." She slams the folder on the table while craning her neck to undo some of her tension. "Explain."

"Sherlock Holmes can detect a lie even if you don't open your mouth. The cover has to be as close to the truth." Natasha starts. "I can be discreet but you; anyone can read you with one look and dismiss you immediately. "

Molly shoots her an indignant glare and was about to run her mouth off to protest.

Natasha cuts her off before she does. "Let me finish…"

Molly backs down and falls on the stool again.

"Which is why I recommended you. SHIELD knows you're brilliant or at least anyone who's worked with you knows. But if you recall, people used to look over you because you have a presence of a mouse. We don't need stealth, we need invisibility."

Molly still rolls her eyes. "You basically insulted and complimented me right there. I know that and I've used it on previous missions too. But this cover, which by the way is not a cover, will open doors that I have locked and have thrown away the keys to. And at the possibility of a blown cover, I will have to change my name so as not to turn up in MI-5's list of persons of interest. His brother is the British Government. There's nothing in the SHIELD handbook about that!"

"Alright Doctor Goody-Two-Shoes, me and Clint will devise the exit strategy if it comes to that point. Don't sweat the small stuff. This will be cake." Natasha easily brushes off Molly's overreaction.

"I don't have a choice, do I?" Molly's shoulders droop in defeat.

"If it were up to me, maybe… But it's from the man upstairs." Natasha covers her left eye with her left hand to simulate the eye patch.

Molly stifled a giggle, trying not to laugh at it. "Pffft! You're a shitty friend, you know that? Hahaha!" She unsuccessfully stops herself from letting out a guffaw. Her laughter rings out in the lab, finally just letting her apprehensions go.

Natasha smiles and pats her back as the cackling doctor chokes a bit from her uncontrolled laughter.

"I'll use that next time I reference the Director to Agent Hand. I might get an actual laugh from her." Molly goes down to giggling as she calms herself from her outburst.

"Oh, I need proof when you catch her doing it. I don't think I've even seen that woman smile before." Natasha stands from the stool to take her leave. "We'll start tomorrow. I suggest you find those keys you threw away. You'll be taking them back to London with you."

_**tbc**_


End file.
